One possible plot could be that Alex Mercer from Prototype finds himself in the Naruto universe. He could be mistaken for a powerful rogue ninja at first. Then, he starts to learn about chakra and how it differs from his own abilities. He might end up teaming with Naruto to fight a common enemy like Orochimaru, who is interested in Mercer's regenerative abilities for his own dark experiments.
One possible plot could be that Alex Mercer (from Prototype) somehow ends up in the Naruto world. He could be initially seen as a threat due to his shape - shifting abilities. Naruto, being the curious and friendly ninja he is, tries to understand Mercer instead of attacking him right away. They could team up against a common enemy, like a powerful new Akatsuki member who has powers similar to Mercer's virus - like abilities. This would force Mercer to use his combat skills and Naruto to use his ninja techniques in a new and combined way.
Perhaps in the crossover, the Prototype virus could somehow infect the magical creatures in the Harry Potter universe. This would lead to a crisis where normal spells and magic can't stop the infected creatures. Harry and his friends would have to seek help from Mercer, who understands the virus. Together, they could try to find a way to either cure the infected or contain the spread. Mercer might use his own knowledge of the virus and his powers to fight the infected creatures, while Harry uses his magic skills to protect Mercer from magical attacks.
Well, perhaps in this fanfiction, the SAO system is corrupted by an Orochimaru - like figure. He wants to use the virtual world to gain power and immortality. Naruto and his friends, along with the SAO players, have to team up. Naruto's positive attitude and never - give - up spirit inspire the SAO players. They all work together to defeat this new threat, with Naruto using his Rasengan in new and creative ways within the SAO world.
A plot could involve the Killzone characters getting access to chakra. Some of the Killzone soldiers might start to learn ninjutsu and this causes chaos in their own military structure. Meanwhile, Naruto has to figure out how to get back to his own world while also dealing with the new threats that this crossover has created. Maybe he teams up with some of the more honorable Killzone soldiers to find a solution.
A plot might involve Naruto being sent to Bayonetta's world. He'd be out of his element, but his determination would shine through. Bayonetta could mistake him for a strange demon at first. However, they soon realize they can help each other. Naruto's chakra could interact in unexpected ways with Bayonetta's magic. Together, they could face off against Bayonetta's foes, like the angels, with Naruto's Rasengan combined with Bayonetta's Witch Time abilities making for some epic battles.
In a Naruto and Spiderman crossover, it could start with Spiderman noticing some strange energy signatures in his city. These turn out to be Naruto's chakra flares. Naruto is there looking for a way back to his own world after being accidentally sent to Earth - 616 (the Marvel Universe). They meet and at first don't understand each other. However, when they see a common enemy, a group of ninjas - like mutants who are causing chaos, they decide to work together. Spiderman uses his agility and web - shooting while Naruto uses his jutsu to defeat the bad guys.
One possible plot could be that Naruto and his team are on a mission in a strange new land that turns out to be the world of Claymore. They encounter Claymores, the half - human, half - yoma warriors. Naruto, with his never - give - up attitude, tries to understand the complex relationship between humans and yoma in this world. He could end up befriending some of the Claymores and together they fight against a powerful common enemy that threatens both their worlds.
One possible plot could be that Naruto, while on a mission, somehow gets transported to the world of Undertale. He teams up with Frisk to stop Flowey from taking over both their worlds. Naruto's ninja skills, like his shadow clones, could be used in creative ways in the battles against the monsters in Undertale.
One possible plot could be that Guts from Berserk is somehow transported to the Naruto universe. He might initially be seen as a threat due to his menacing appearance and his large sword. However, as the story progresses, he could team up with Naruto and his friends to fight against a common enemy, like an Akatsuki member who has acquired some of the dark magic from the Berserk world. Guts' fighting skills and his ability to face the most terrifying foes could inspire Naruto and give him new perspectives on combat.
One possible plot could be that Spyro, being a powerful dragon from his own realm, somehow gets transported to the Naruto universe. He could initially be seen as a strange and powerful creature. Naruto and his friends might be both cautious and intrigued. Spyro could use his fire - breathing and flying abilities to help the Leaf Village in a battle against a common enemy, like a powerful group of rogue ninjas or a new, mysterious threat that the village alone couldn't handle. As they fight together, Spyro could learn about chakra and the ninja way, while Naruto and his friends could learn about Spyro's world and its magic.